
import dataclasses
import re
import string
from typing import Any, Dict, Iterator, List, Mapping, Optional, Sequence, Tuple

import numpy as np

from . import residue_constants


__lowerCAmelCase     :	Dict       			=  Mapping[str, np.ndarray]
__lowerCAmelCase     :	Any       			=  Mapping[str, Any]  # Is a nested dict.
__lowerCAmelCase     :	Optional[Any]       			=  0.01




@dataclasses.dataclass(frozen=_A	)
class 			UpperCAmelCase_     :


  '''simple docstring'''







  a__       			=						42  # [num_res, num_atom_type, 3]

  # Amino-acid type for each residue represented as an integer between 0 and
  # 20, where 20 is 'X'.
  a__       			=						42  # [num_res]

  # Binary float mask to indicate presence of a particular atom. 1.0 if an atom
  # is present and 0.0 if not. This should be used for loss masking.
  a__       			=						42  # [num_res, num_atom_type]

  # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
  a__       			=						42  # [num_res]

  # B-factors, or temperature factors, of each residue (in sq. angstroms units),
  # representing the displacement of the residue from its ground truth mean
  # value.
  a__       			=						42  # [num_res, num_atom_type]

  # Chain indices for multi-chain predictions
  a__       			=						None

  # Optional remark about the protein. Included as a comment in output PDB
  # files
  a__       			=						None

  # Templates used to generate this protein (prediction-only)
  a__       			=						None

  # Chain corresponding to each parent
  a__       			=						None







def a__       (			A_   ):






  '''simple docstring'''





  __magic_name__								=			R"""(\[[A-Z]+\]\n)"""
  __magic_name__								=			[tag.strip() for tag in re.split(A_,	A_   ) if len(A_   ) > 0]
  __magic_name__								=			zip(tags[0::2],	[l.split("""\n"""   ) for l in tags[1::2]]   )

  __magic_name__								=			["N", "CA", "C"]
  __magic_name__								=			None
  __magic_name__								=			None
  __magic_name__								=			None
  for g in groups:
    if "[PRIMARY]" == g[0]:
      __magic_name__								=			g[1][0].strip()
      for i in range(len(A_   )   ):
        if seq[i] not in residue_constants.restypes:
          __magic_name__								=			"""X"""  # FIXME: strings are immutable
      __magic_name__								=			np.array(
          [residue_constants.restype_order.get(A_,	residue_constants.restype_num   ) for res_symbol in seq]   )
    elif "[TERTIARY]" == g[0]:
      __magic_name__								=			[]
      for axis in range(3   ):
        tertiary.append(list(map(A_,	g[1][axis].split()   )   )   )
      __magic_name__								=			np.array(A_   )
      __magic_name__								=			np.zeros((len(tertiary[0]   ) // 3, residue_constants.atom_type_num, 3)   ).astype(np.floataa   )
      for i, atom in enumerate(A_   ):
        __magic_name__								=			np.transpose(tertiary_np[:, i::3]   )
      atom_positions *= PICO_TO_ANGSTROM
    elif "[MASK]" == g[0]:
      __magic_name__								=			np.array(list(map({"""-""": 0, """+""": 1}.get,	g[1][0].strip()   )   )   )
      __magic_name__								=			np.zeros(
          (
              len(A_   ),
              residue_constants.atom_type_num,
          )   ).astype(np.floataa   )
      for i, atom in enumerate(A_   ):
        __magic_name__								=			1
      atom_mask *= mask[..., None]

  assert aatype is not None

  return Protein(
      atom_positions=A_,	atom_mask=A_,	aatype=A_,	residue_index=np.arange(len(A_   )   ),	b_factors=A_,	)

def a__       (			A_,	A_ = 0   ):






  '''simple docstring'''





  __magic_name__								=			[]

  __magic_name__								=			prot.remark
  if remark is not None:
    pdb_headers.append(f'''REMARK {remark}'''   )

  __magic_name__								=			prot.parents
  __magic_name__								=			prot.parents_chain_index
  if parents is not None and parents_chain_index is not None:
    __magic_name__								=			[p for i, p in zip(A_,	A_   ) if i == chain_id]

  if parents is None or len(A_   ) == 0:
    __magic_name__								=			["""N/A"""]

  pdb_headers.append(f'''PARENT {' '.join(A_   )}'''   )

  return pdb_headers

def a__       (			A_,	A_   ):






  '''simple docstring'''





  __magic_name__								=			[]
  __magic_name__								=			pdb_str.split("""\n"""   )

  __magic_name__								=			prot.remark
  if remark is not None:
    out_pdb_lines.append(f'''REMARK {remark}'''   )

  __magic_name__								=			42
  if prot.parents is not None and len(prot.parents   ) > 0:
    __magic_name__								=			[]
    if prot.parents_chain_index is not None:
      __magic_name__								=			{}
      for p, i in zip(prot.parents,	prot.parents_chain_index   ):
        parent_dict.setdefault(str(A_   ),	[]   )
        parent_dict[str(A_   )].append(A_   )

      __magic_name__								=			max([int(A_   ) for chain_idx in parent_dict]   )
      for i in range(max_idx + 1   ):
        __magic_name__								=			parent_dict.get(str(A_   ),	["""N/A"""]   )
        parents_per_chain.append(A_   )
    else:
      parents_per_chain.append(list(prot.parents   )   )
  else:
    __magic_name__								=			[["""N/A"""]]

  def make_parent_line(A_   ) -> str:
    return f'''PARENT {' '.join(A_   )}'''

  out_pdb_lines.append(make_parent_line(parents_per_chain[0]   )   )

  __magic_name__								=			0
  for i, l in enumerate(A_   ):
    if "PARENT" not in l and "REMARK" not in l:
      out_pdb_lines.append(A_   )
    if "TER" in l and "END" not in lines[i + 1]:
      chain_counter += 1
      if not chain_counter >= len(A_   ):
        __magic_name__								=			parents_per_chain[chain_counter]
      else:
        __magic_name__								=			["""N/A"""]

      out_pdb_lines.append(make_parent_line(A_   )   )

  return "\n".join(A_   )

def a__       (			A_   ):






  '''simple docstring'''





  __magic_name__								=			residue_constants.restypes + ["""X"""]

  def res_atoa(A_   ) -> str:
    return residue_constants.restype_atoa.get(restypes[r],	"""UNK"""   )

  __magic_name__								=			residue_constants.atom_types

  __magic_name__								=			[]

  __magic_name__								=			prot.atom_mask
  __magic_name__								=			prot.aatype
  __magic_name__								=			prot.atom_positions
  __magic_name__								=			prot.residue_index.astype(np.intaa   )
  __magic_name__								=			prot.b_factors
  __magic_name__								=			prot.chain_index

  if np.any(aatype > residue_constants.restype_num   ):
    raise ValueError("""Invalid aatypes."""   )

  __magic_name__								=			get_pdb_headers(A_   )
  if len(A_   ) > 0:
    pdb_lines.extend(A_   )

  __magic_name__								=			aatype.shape[0]
  __magic_name__								=			1
  __magic_name__								=			0
  __magic_name__								=			string.ascii_uppercase
  __magic_name__								=			None
  # Add all atom sites.
  for i in range(A_   ):
    __magic_name__								=			res_atoa(aatype[i]   )
    for atom_name, pos, mask, b_factor in zip(A_,	atom_positions[i],	atom_mask[i],	b_factors[i]   ):
      if mask < 0.5:
        continue

      __magic_name__								=			"""ATOM"""
      __magic_name__								=			atom_name if len(A_   ) == 4 else f''' {atom_name}'''
      __magic_name__								=			""""""
      __magic_name__								=			""""""
      __magic_name__								=			1.00
      __magic_name__								=			atom_name[0]  # Protein supports only C, N, O, S, this works.
      __magic_name__								=			""""""

      __magic_name__								=			"""A"""
      if chain_index is not None:
        __magic_name__								=			chain_tags[chain_index[i]]

      # PDB is a columnar format, every space matters here!
      __magic_name__								=			(
          f'''{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}'''
          f'''{res_name_a:>3} {chain_tag:>1}'''
          f'''{residue_index[i]:>4}{insertion_code:>1}   '''
          f'''{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}'''
          f'''{occupancy:>6.2f}{b_factor:>6.2f}          '''
          f'''{element:>2}{charge:>2}'''
      )
      pdb_lines.append(A_   )
      atom_index += 1

    __magic_name__								=			i == n - 1
    if chain_index is not None:
      if i != n - 1 and chain_index[i + 1] != prev_chain_index:
        __magic_name__								=			True
        __magic_name__								=			chain_index[i + 1]

    if should_terminate:
      # Close the chain.
      __magic_name__								=			"""TER"""
      __magic_name__								=			(
          f'''{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]   ):>3} {chain_tag:>1}{residue_index[i]:>4}'''
      )
      pdb_lines.append(A_   )
      atom_index += 1

      if i != n - 1:
        # "prev" is a misnomer here. This happens at the beginning of
        # each new chain.
        pdb_lines.extend(get_pdb_headers(A_,	A_   )   )

  pdb_lines.append("""END"""   )
  pdb_lines.append(""""""   )
  return "\n".join(A_   )

def a__       (			A_   ):






  '''simple docstring'''





  return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def a__       (			A_,	A_,	A_ = None,	A_ = None,	A_ = None,	A_ = None,	A_ = None,	):






  '''simple docstring'''





  return Protein(
      aatype=features["""aatype"""],	atom_positions=result["""final_atom_positions"""],	atom_mask=result["""final_atom_mask"""],	residue_index=features["""residue_index"""] + 1,	b_factors=b_factors if b_factors is not None else np.zeros_like(result["""final_atom_mask"""]   ),	chain_index=A_,	remark=A_,	parents=A_,	parents_chain_index=A_,	)



def a__       (			A_   ):






  '''simple docstring'''





  if len(A_   ) < 2:
    return collection

  def circle_sort_util(A_,	A_,	A_   ) -> bool:
    __magic_name__								=			False

    if low == high:
      return swapped

    __magic_name__								=			low
    __magic_name__								=			high

    while left < right:
      if collection[left] > collection[right]:
        __magic_name__	,       __magic_name__								=			(
            collection[right],
            collection[left],
        )
        __magic_name__								=			True

      left += 1
      right -= 1

    if left == right and collection[left] > collection[right + 1]:
      __magic_name__	,       __magic_name__								=			(
          collection[right + 1],
          collection[left],
      )

      __magic_name__								=			True

    __magic_name__								=			low + int((high - low) / 2   )
    __magic_name__								=			circle_sort_util(A_,	A_,	A_   )
    __magic_name__								=			circle_sort_util(A_,	mid + 1,	A_   )

    return swapped or left_swap or right_swap

  __magic_name__								=			True

  while is_not_sorted is True:
    __magic_name__								=			circle_sort_util(A_,	0,	len(A_   ) - 1   )

  return collection


if __name__ == "__main__":
    __lowerCAmelCase     :	Union[str, Any]       			=  input('Enter numbers separated by a comma:\n').strip()
    __lowerCAmelCase     :	Tuple       			=  [int(item) for item in user_input.split(',')]
    print(circle_sort(unsorted))

